[3dem] FSC validation server

Ardan Patwardhan ardan at ebi.ac.uk
Mon Oct 21 08:29:40 PDT 2013

Dear all


PDBe is in the process of developing a range of web-based validation
services for the benefit of the EM community. Our aim is to promote and
encourage good practices and consistency in reporting results - we currently
have fewer than 15 FSC curves in EMDB! As a first step in this process we
now have an FSC server in beta testing:

To use this service you will need to upload two maps and specify the voxel
size - it will then calculate the FSC curve and present this result as a
plot. It will also calculate and show the 0.5, 0.333 and 0.143 cut-off
resolutions (calculated by linear interpolation from the FSC curve), and it
will generate an XML file that can be uploaded as part of an EMDB


Note: This server does not require any login and is not a part of EMDB
deposition so you can use on any data irrespective of whether you plan to
submit it to EMDB or not. Additionally, the beta testing server is fully
functional and the XML files generated can be uploaded to EMDB.


In order to go from beta to a production version we need your help in
testing the resource!


We are interested in feedback on both technical and scientific aspects of
the resource, e.g.:

a) sanity check - does this server produce the same results that you get
from other software?

b) what additional information should we collect from the user? (protocol -
"gold standard", odd/even etc; symmetry; masking)

c) should we display and calculate other cut-offs?

d) file format issues

e) file size issues

f) features that you would like implemented and any bugs you encounter


We would also like to offer a few more test sets for the FSC server. We are
thankful for any pairs of maps you are willing to give us to make publicly
available as test data for FSC server.


Please feel free to contact me with feedback and questions: ardan at ebi.ac.uk


Many thanks and best wishes


Ardan Patwardhan

European Bioinformatics Institute (EMBL-EBI) European Molecular Biology

Wellcome Trust Genome Campus

Hinxton, Cambridge CB10 1SD, UK
Tel: +44 1223 492649



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